Running: ./testmodel.py --libraries=/home/hudson/saved_omc/libraries/.openmodelica/libraries --ompython_omhome=/usr Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.conf.json
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo): time 0.0009008/0.0009008, allocations: 104.3 kB / 19.7 MB, free: 444 kB / 13.93 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo): time 0.0009472/0.0009472, allocations: 216.9 kB / 23 MB, free: 2.965 MB / 13.93 MB
"
[Timeout remaining time 180]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo", uses=false) [Timeout 180]
"Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo): time 0.9902/0.9902, allocations: 230.6 MB / 256.8 MB, free: 9.621 MB / 202.7 MB
"
[Timeout remaining time 179]
loadFile("/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo", uses=false) [Timeout 180]
"[/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/Examples/package.order:0:0-0:0:readonly] Warning: The package.order file does not list all .mo files and directories (containing package.mo) present in its directory.
Missing names are:
	Paracetamol_Experiment
Notification: Performance of loadFile(/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo): time 1.801/1.801, allocations: 334.2 MB / 0.6323 GB, free: 7.879 MB / 442.7 MB
"
[Timeout remaining time 178]
Using package Pharmacolibrary with version 25.09 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Pharmacolibrary 25.9.0/package.mo)
Using package Modelica with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Modelica 4.1.0+maint.om/package.mo)
Using package Complex with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/Complex 4.1.0+maint.om/package.mo)
Using package ModelicaServices with version 4.1.0 (/home/hudson/saved_omc/libraries/.openmodelica/libraries/ModelicaServices 4.1.0+maint.om/package.mo)
Running command: translateModel(Pharmacolibrary.Examples.PK_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin")
translateModel(Pharmacolibrary.Examples.PK_1C_Gentamicin,tolerance=1e-06,outputFormat="empty",numberOfIntervals=86400,variableFilter="",fileNamePrefix="Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin") [Timeout 660]
"Notification: Pharmacolibrary requested package Modelica of version 4.0.0. Modelica 4.1.0 is used instead which states that it is fully compatible without conversion script needed.
Notification: Performance of FrontEnd - loaded program: time 0.001656/0.001656, allocations: 67.88 kB / 0.867 GB, free: 7.984 MB / 0.573 GB
Notification: Performance of FrontEnd - Absyn->SCode: time 0.1701/0.1718, allocations: 112.8 MB / 0.9772 GB, free: 6.902 MB / 0.6824 GB
Notification: Performance of NFInst.instantiate(Pharmacolibrary.Examples.PK_1C_Gentamicin): time 0.00255/0.1743, allocations: 2.016 MB / 0.9792 GB, free: 4.875 MB / 0.6824 GB
Notification: Performance of NFInst.instExpressions: time 0.000844/0.1752, allocations: 0.5221 MB / 0.9797 GB, free: 4.352 MB / 0.6824 GB
Notification: Performance of NFInst.updateImplicitVariability: time 8.082e-05/0.1753, allocations: 4 kB / 0.9797 GB, free: 4.348 MB / 0.6824 GB
Notification: Performance of NFTyping.typeComponents: time 0.0001147/0.1754, allocations: 19.78 kB / 0.9797 GB, free: 4.328 MB / 0.6824 GB
Notification: Performance of NFTyping.typeBindings: time 0.0001378/0.1755, allocations: 47.56 kB / 0.9797 GB, free: 4.281 MB / 0.6824 GB
Notification: Performance of NFTyping.typeClassSections: time 0.0001778/0.1757, allocations: 55.88 kB / 0.9798 GB, free: 4.227 MB / 0.6824 GB
Notification: Performance of NFFlatten.flatten: time 0.0002127/0.1759, allocations: 191.1 kB / 0.98 GB, free: 4.039 MB / 0.6824 GB
Notification: Performance of NFFlatten.resolveConnections: time 0.0001206/0.176, allocations: 37.95 kB / 0.98 GB, free: 3.996 MB / 0.6824 GB
Notification: Performance of NFEvalConstants.evaluate: time 0.0001003/0.1761, allocations: 67.78 kB / 0.9801 GB, free: 3.93 MB / 0.6824 GB
Notification: Performance of NFSimplifyModel.simplify: time 0.0001044/0.1762, allocations: 79.55 kB / 0.9802 GB, free: 3.852 MB / 0.6824 GB
Notification: Performance of NFPackage.collectConstants: time 2.476e-05/0.1763, allocations: 12 kB / 0.9802 GB, free: 3.84 MB / 0.6824 GB
Notification: Performance of NFFlatten.collectFunctions: time 2.205e-05/0.1763, allocations: 16 kB / 0.9802 GB, free: 3.824 MB / 0.6824 GB
Notification: Performance of NFScalarize.scalarize: time 3.141e-05/0.1763, allocations: 27.92 kB / 0.9802 GB, free: 3.797 MB / 0.6824 GB
Notification: Performance of NFVerifyModel.verify: time 6.889e-05/0.1764, allocations: 67.72 kB / 0.9803 GB, free: 3.73 MB / 0.6824 GB
Notification: Performance of NFConvertDAE.convert: time 0.0001888/0.1766, allocations: 163.4 kB / 0.9804 GB, free: 3.57 MB / 0.6824 GB
Notification: Performance of FrontEnd - DAE generated: time 4.118e-06/0.1766, allocations: 0 / 0.9804 GB, free: 3.57 MB / 0.6824 GB
Notification: Performance of FrontEnd: time 2.194e-06/0.1766, allocations: 4 kB / 0.9804 GB, free: 3.566 MB / 0.6824 GB
Notification: Performance of Transformations before backend: time 5.981e-06/0.1766, allocations: 4 kB / 0.9804 GB, free: 3.562 MB / 0.6824 GB
Notification: Model statistics after passing the front-end and creating the data structures used by the back-end:
 * Number of equations: 26
 * Number of variables: 26
Notification: Performance of Generate backend data structure: time 0.0006398/0.1772, allocations: 440.8 kB / 0.9809 GB, free: 3.09 MB / 0.6824 GB
Notification: Performance of prepare preOptimizeDAE: time 3.694e-05/0.1773, allocations: 10.11 kB / 0.9809 GB, free: 3.082 MB / 0.6824 GB
Notification: Performance of preOpt normalInlineFunction (simulation): time 4.924e-05/0.1773, allocations: 20.84 kB / 0.9809 GB, free: 3.062 MB / 0.6824 GB
Notification: Performance of preOpt evaluateParameters (simulation): time 0.0002559/0.1776, allocations: 184.2 kB / 0.9811 GB, free: 2.859 MB / 0.6824 GB
Notification: Performance of preOpt simplifyIfEquations (simulation): time 1.298e-05/0.1776, allocations: 11.94 kB / 0.9811 GB, free: 2.848 MB / 0.6824 GB
Notification: Performance of preOpt expandDerOperator (simulation): time 3.27e-05/0.1776, allocations: 16 kB / 0.9811 GB, free: 2.832 MB / 0.6824 GB
Notification: Performance of preOpt clockPartitioning (simulation): time 0.0002191/0.1778, allocations: 155.3 kB / 0.9812 GB, free: 2.668 MB / 0.6824 GB
Notification: Performance of preOpt findStateOrder (simulation): time 1.346e-05/0.1778, allocations: 7.953 kB / 0.9813 GB, free: 2.66 MB / 0.6824 GB
Notification: Performance of preOpt replaceEdgeChange (simulation): time 1.402e-05/0.1778, allocations: 4 kB / 0.9813 GB, free: 2.656 MB / 0.6824 GB
Notification: Performance of preOpt inlineArrayEqn (simulation): time 5.912e-06/0.1779, allocations: 4 kB / 0.9813 GB, free: 2.652 MB / 0.6824 GB
Notification: Performance of preOpt removeEqualRHS (simulation): time 0.0001838/0.178, allocations: 129.5 kB / 0.9814 GB, free: 2.52 MB / 0.6824 GB
Notification: Performance of preOpt removeSimpleEquations (simulation): time 0.0004966/0.1785, allocations: 360.2 kB / 0.9817 GB, free: 2.137 MB / 0.6824 GB
Notification: Performance of preOpt comSubExp (simulation): time 0.0002448/0.1788, allocations: 172.2 kB / 0.9819 GB, free: 1.953 MB / 0.6824 GB
Notification: Performance of preOpt resolveLoops (simulation): time 9.77e-05/0.1789, allocations: 82.53 kB / 0.982 GB, free: 1.863 MB / 0.6824 GB
Notification: Performance of preOpt evalFunc (simulation): time 1.37e-05/0.1789, allocations: 4.141 kB / 0.982 GB, free: 1.859 MB / 0.6824 GB
Notification: Performance of preOpt encapsulateWhenConditions (simulation): time 0.000236/0.1791, allocations: 226.8 kB / 0.9822 GB, free: 1.609 MB / 0.6824 GB
Notification: Performance of pre-optimization done (n=20): time 2.324e-06/0.1791, allocations: 3.938 kB / 0.9822 GB, free: 1.605 MB / 0.6824 GB
Notification: Performance of matching and sorting (n=21): time 0.0009668/0.1801, allocations: 0.6728 MB / 0.9828 GB, free: 0.8711 MB / 0.6824 GB
Notification: Performance of inlineWhenForInitialization (initialization): time 5.572e-05/0.1802, allocations: 140.5 kB / 0.983 GB, free: 0.7031 MB / 0.6824 GB
Notification: Performance of selectInitializationVariablesDAE (initialization): time 0.0001117/0.1803, allocations: 164.7 kB / 0.9831 GB, free: 0.5352 MB / 0.6824 GB
Notification: Performance of collectPreVariables (initialization): time 1.718e-05/0.1803, allocations: 29.7 kB / 0.9832 GB, free: 0.5 MB / 0.6824 GB
Notification: Performance of collectInitialEqns (initialization): time 5.512e-05/0.1803, allocations: 108.5 kB / 0.9833 GB, free: 400 kB / 0.6824 GB
Notification: Performance of collectInitialBindings (initialization): time 3.797e-05/0.1804, allocations: 67.42 kB / 0.9833 GB, free: 332 kB / 0.6824 GB
Notification: Performance of simplifyInitialFunctions (initialization): time 5.416e-05/0.1804, allocations: 49.7 kB / 0.9834 GB, free: 276 kB / 0.6824 GB
Notification: Performance of setup shared object (initialization): time 9.234e-05/0.1805, allocations: 338.8 kB / 0.9837 GB, free: 15.93 MB / 0.698 GB
Notification: Performance of preBalanceInitialSystem (initialization): time 0.0001449/0.1807, allocations: 132.7 kB / 0.9838 GB, free: 15.78 MB / 0.698 GB
Notification: Performance of partitionIndependentBlocks (initialization): time 0.0001566/0.1808, allocations: 214.1 kB / 0.984 GB, free: 15.54 MB / 0.698 GB
Notification: Performance of analyzeInitialSystem (initialization): time 0.0005378/0.1814, allocations: 0.504 MB / 0.9845 GB, free: 14.97 MB / 0.698 GB
Notification: Performance of solveInitialSystemEqSystem (initialization): time 2.655e-06/0.1814, allocations: 0 / 0.9845 GB, free: 14.97 MB / 0.698 GB
Notification: Performance of matching and sorting (n=32) (initialization): time 0.0003674/0.1817, allocations: 382.2 kB / 0.9849 GB, free: 14.57 MB / 0.698 GB
Notification: Performance of prepare postOptimizeDAE: time 3.961e-05/0.1818, allocations: 63.41 kB / 0.985 GB, free: 14.49 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (initialization): time 6.853e-06/0.1818, allocations: 4 kB / 0.985 GB, free: 14.49 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (initialization): time 1.585e-05/0.1818, allocations: 0 / 0.985 GB, free: 14.49 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (initialization): time 0.0001298/0.1819, allocations: 47.91 kB / 0.985 GB, free: 14.44 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (initialization): time 1.012e-05/0.1819, allocations: 11.92 kB / 0.985 GB, free: 14.43 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (initialization): time 8.682e-05/0.182, allocations: 12 kB / 0.985 GB, free: 14.42 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (initialization): time 1.564e-05/0.182, allocations: 15.98 kB / 0.985 GB, free: 14.4 MB / 0.698 GB
Warning: Assuming fixed start value for the following 6 variables:
         singleDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         singleDose.variableDose.TotalCumulativeMass:VARIABLE(min = -1e-12 unit = \"kg\" fixed = true )  \"Total dose adminitrated by this source\" type: Real
         central.AUC:VARIABLE(unit = \"kg.s/m3\" fixed = true )  \"area under curve\" type: Real
         central.Cmin:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         central.Cmax:DISCRETE(min = -1e-9 unit = \"kg/m3\" fixed = true )  type: Real
         central.rising:DISCRETE(fixed = true protected = true )  type: Boolean
Notification: Model statistics after passing the back-end for initialization:
 * Number of independent subsystems: 7
 * Number of states: 0 ()
 * Number of discrete variables: 13 ($PRE.central.Cmin,central.Cmin,$PRE.central.Cmax,central.Cmax,$PRE.central.rising,$PRE.singleDose.pulse.count,$PRE.singleDose.pulse.T_start,central.rising,singleDose.pulse.count,singleDose.pulse.T_start,$whenCondition3,$whenCondition2,$whenCondition1)
 * Number of discrete states: 0 ()
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for initialization (30):
 * Single equations (assignments): 28
 * Array equations: 0
 * Algorithm blocks: 2
 * Record equations: 0
 * When equations: 0
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of prepare postOptimizeDAE: time 0.0001779/0.1822, allocations: 197.6 kB / 0.9852 GB, free: 14.2 MB / 0.698 GB
Notification: Performance of postOpt lateInlineFunction (simulation): time 2.174e-05/0.1822, allocations: 19.84 kB / 0.9852 GB, free: 14.18 MB / 0.698 GB
Notification: Performance of postOpt wrapFunctionCalls (simulation): time 3.101e-05/0.1823, allocations: 25.28 kB / 0.9853 GB, free: 14.16 MB / 0.698 GB
Notification: Performance of postOpt inlineArrayEqn (simulation): time 3.457e-06/0.1823, allocations: 3.984 kB / 0.9853 GB, free: 14.15 MB / 0.698 GB
Notification: Performance of postOpt constantLinearSystem (simulation): time 5.33e-06/0.1823, allocations: 0 / 0.9853 GB, free: 14.15 MB / 0.698 GB
Notification: Performance of postOpt simplifysemiLinear (simulation): time 3.637e-06/0.1823, allocations: 0 / 0.9853 GB, free: 14.15 MB / 0.698 GB
Notification: Performance of postOpt removeSimpleEquations (simulation): time 0.0004912/0.1828, allocations: 0.5095 MB / 0.9858 GB, free: 13.59 MB / 0.698 GB
Notification: Performance of postOpt simplifyComplexFunction (simulation): time 2.285e-06/0.1828, allocations: 0 / 0.9858 GB, free: 13.59 MB / 0.698 GB
Notification: Performance of postOpt solveSimpleEquations (simulation): time 0.0001146/0.1829, allocations: 39.91 kB / 0.9858 GB, free: 13.55 MB / 0.698 GB
Notification: Performance of postOpt tearingSystem (simulation): time 2.274e-06/0.1829, allocations: 0 / 0.9858 GB, free: 13.55 MB / 0.698 GB
Notification: Performance of postOpt inputDerivativesUsed (simulation): time 1.573e-05/0.1829, allocations: 11.94 kB / 0.9858 GB, free: 13.54 MB / 0.698 GB
Notification: Performance of postOpt calculateStrongComponentJacobians (simulation): time 1.984e-06/0.1829, allocations: 4 kB / 0.9858 GB, free: 13.54 MB / 0.698 GB
Notification: Performance of postOpt calculateStateSetsJacobians (simulation): time 1.714e-06/0.1829, allocations: 0 / 0.9858 GB, free: 13.54 MB / 0.698 GB
Notification: Performance of postOpt symbolicJacobian (simulation): time 0.0004325/0.1833, allocations: 480.8 kB / 0.9863 GB, free: 13.03 MB / 0.698 GB
Notification: Performance of postOpt removeConstants (simulation): time 1.949e-05/0.1834, allocations: 15.89 kB / 0.9863 GB, free: 13.02 MB / 0.698 GB
Notification: Performance of postOpt simplifyTimeIndepFuncCalls (simulation): time 2.628e-05/0.1834, allocations: 8.062 kB / 0.9863 GB, free: 13.01 MB / 0.698 GB
Notification: Performance of postOpt simplifyAllExpressions (simulation): time 7.64e-05/0.1835, allocations: 11.98 kB / 0.9863 GB, free: 13 MB / 0.698 GB
Notification: Performance of postOpt findZeroCrossings (simulation): time 5.873e-05/0.1835, allocations: 15.97 kB / 0.9863 GB, free: 12.98 MB / 0.698 GB
Notification: Performance of postOpt collapseArrayExpressions (simulation): time 1.151e-05/0.1835, allocations: 8 kB / 0.9863 GB, free: 12.97 MB / 0.698 GB
Notification: Performance of sorting global known variables: time 6.924e-05/0.1836, allocations: 131.1 kB / 0.9865 GB, free: 12.84 MB / 0.698 GB
Notification: Performance of sort global known variables: time 5e-08/0.1836, allocations: 3.938 kB / 0.9865 GB, free: 12.84 MB / 0.698 GB
Notification: Performance of remove unused functions: time 0.0001948/0.1838, allocations: 44 kB / 0.9865 GB, free: 12.8 MB / 0.698 GB
Notification: Model statistics after passing the back-end for simulation:
 * Number of independent subsystems: 1
 * Number of states: 5 (singleDose.TotalCumulativeMass,singleDose.variableDose.TotalCumulativeMass,central.C,central.AUC,elim.MExc)
 * Number of discrete variables: 8 ($whenCondition1,$whenCondition2,$whenCondition3,singleDose.pulse.T_start,singleDose.pulse.count,central.Cmax,central.Cmin,central.rising)
 * Number of discrete states: 6 (singleDose.pulse.count,central.Cmin,$whenCondition3,central.Cmax,$whenCondition2,central.rising)
 * Number of clocked states: 0 ()
 * Top-level inputs: 0
Notification: Strong component statistics for simulation (18):
 * Single equations (assignments): 15
 * Array equations: 0
 * Algorithm blocks: 1
 * Record equations: 0
 * When equations: 2
 * If-equations: 0
 * Equation systems (not torn): 0
 * Torn equation systems: 0
 * Mixed (continuous/discrete) equation systems: 0
Notification: Performance of Backend phase and start with SimCode phase: time 8.559e-05/0.1839, allocations: 103.2 kB / 0.9866 GB, free: 12.69 MB / 0.698 GB
Notification: Performance of simCode: created initialization part: time 0.0003496/0.1842, allocations: 367.7 kB / 0.987 GB, free: 12.29 MB / 0.698 GB
Notification: Performance of simCode: created event and clocks part: time 1.532e-06/0.1842, allocations: 384 / 0.987 GB, free: 12.29 MB / 0.698 GB
Notification: Performance of simCode: created simulation system equations: time 0.0001409/0.1844, allocations: 178.4 kB / 0.9871 GB, free: 12.09 MB / 0.698 GB
Notification: Performance of simCode: created of all other equations (e.g. parameter, nominal, assert, etc): time 0.0002812/0.1847, allocations: 47.97 kB / 0.9872 GB, free: 12.05 MB / 0.698 GB
Notification: Performance of simCode: created linear, non-linear and system jacobian parts: time 0.0008554/0.1855, allocations: 0.6842 MB / 0.9878 GB, free: 11.32 MB / 0.698 GB
Notification: Performance of simCode: some other stuff during SimCode phase: time 8.072e-05/0.1856, allocations: 107.4 kB / 0.988 GB, free: 11.2 MB / 0.698 GB
Notification: Performance of simCode: all other stuff during SimCode phase: time 4.584e-05/0.1856, allocations: 23.44 kB / 0.988 GB, free: 11.17 MB / 0.698 GB
Notification: Performance of SimCode: time 9.52e-07/0.1856, allocations: 3.938 kB / 0.988 GB, free: 11.17 MB / 0.698 GB
Notification: Performance of Templates: time 0.003234/0.1889, allocations: 2.359 MB / 0.9903 GB, free: 8.828 MB / 0.698 GB
"
[Timeout remaining time 659]
make -j1 -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.makefile [Timeout 660]
(rm -f Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe ; mkfifo Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe ; head -c 1048576 < Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe >> ../files/Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.sim & ./Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin > Pharmacolibrary_Pharmacolibrary.Examples.PK_1C_Gentamicin.pipe 2>&1) [Timeout 240]
[Calling sys.exit(0), Time elapsed: 7.531596987973899]